Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types

Plyusnin, Ilya; Kant, Ravi; Jääskeläinen, Anne J.; Sironen, Tarja; Vapalahti, Olli; Smura, Teemu

doi:10.1093/ve/veaa091

Cited by 36 publications

(36 citation statements)

References 55 publications

(66 reference statements)

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“…In this study, we identified viral pathogens from ticks infesting dromedary camels in the Makkah province of Saudi Arabia using a metagenomic approach [ 15 ]. Earlier studies have shown that metagenomic approaches can be used to detect both known and novel viruses associated with animal and human diseases [ 16 , 17 ].…”

Section: Introductionmentioning

confidence: 99%

Viral RNA Metagenomics of Hyalomma Ticks Collected from Dromedary Camels in Makkah Province, Saudi Arabia

Zakham

Albalawi

Alanazi

et al. 2021

Viruses

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Arthropod-borne infections are a medical and economic threat to humans and livestock. Over the last three decades, several unprecedented viral outbreaks have been recorded in the Western part of the Arabian Peninsula. However, little is known about the circulation and diversity of arthropod-borne viruses in this region. To prepare for new outbreaks of vector-borne diseases, it is important to detect which viruses circulate in each vector population. In this study, we used a metagenomics approach to characterize the RNA virome of ticks infesting dromedary camels (Camelus dromedaries) in Makkah province, Saudi Arabia. Two hundred ticks of species Hyalomma dromedarii (n = 196) and Hyalomma impeltatum (n = 4) were collected from the Alkhurma district in Jeddah and Al-Taif city. Virome analysis showed the presence of several tick-specific viruses and tick-borne viruses associated with severe illness in humans. Some were identified for the first time in the Arabian Peninsula. The human disease-associated viruses detected included Crimean Congo Hemorrhagic fever virus and Tamdy virus (family Nairoviridae), Guertu virus (family Phenuiviridae), and a novel coltivirus that shares similarities with Tarumizu virus, Tai forest reovirus and Kundal virus (family Reoviridae). Furthermore, Alkhurma hemorrhagic virus (Flaviviridae) was detected in two tick pools by specific qPCR. In addition, tick-specific viruses in families Phenuiviridae (phleboviruses), Iflaviridae, Chuviridae, Totiviridae and Flaviviridae (Pestivirus) were detected. The presence of human pathogenetic viruses warrants further efforts in tick surveillance, xenosurveillence, vector control, and sero-epidemiological investigations in human and animal populations to predict, contain and mitigate future outbreaks in the region.

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Section: Introductionmentioning

confidence: 99%

Viral RNA Metagenomics of Hyalomma Ticks Collected from Dromedary Camels in Makkah Province, Saudi Arabia

Zakham

Albalawi

Alanazi

et al. 2021

Viruses

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“…In any case, it is important to continue improving bioinformatic pipelines and databases to be able to screen rapidly metagenomic data and fully identify the organisms in a sample (Nieuwenhuijse et al, 2020;Plyusnin et al, 2020;Dance, 2021).…”

Section: Discussionmentioning

confidence: 99%

Human and Animal RNA Virus Diversity Detected by Metagenomics in Cameroonian Clams

et al. 2021

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Many recent pandemics have been recognized as zoonotic viral diseases. While their origins remain frequently unknown, environmental contamination may play an important role in emergence. Thus, being able to describe the viral diversity in environmental samples contributes to understand the key issues in zoonotic transmission. This work describes the use of a metagenomic approach to assess the diversity of eukaryotic RNA viruses in river clams and identify sequences from human or potentially zoonotic viruses. Clam samples collected over 2years were first screened for the presence of norovirus to verify human contamination. Selected samples were analyzed using metagenomics, including a capture of sequences from viral families infecting vertebrates (VirCapSeq-VERT) before Illumina NovaSeq sequencing. The bioinformatics analysis included pooling of data from triplicates, quality filtering, elimination of bacterial and host sequences, and a deduplication step before de novo assembly. After taxonomic assignment, the viral fraction represented 0.8–15% of reads with most sequences (68–87%) remaining un-assigned. Yet, several mammalian RNA viruses were identified. Contigs identified as belonging to the Astroviridae were the most abundant, with some nearly complete genomes of bastrovirus identified. Picobirnaviridae sequences were related to strains infecting bats, and few others to strains infecting humans or other hosts. Hepeviridae sequences were mostly related to strains detected in sponge samples but also strains from swine samples. For Caliciviridae and Picornaviridae, most of identified sequences were related to strains infecting bats, with few sequences close to human norovirus, picornavirus, and genogroup V hepatitis A virus. Despite a need to improve the sensitivity of our method, this study describes a large diversity of RNA virus sequences from clam samples. To describe all viral contaminants in this type of food, and being able to identify the host infected by viral sequences detected, may help to understand some zoonotic transmission events and alert health authorities of possible emergence.

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“…For the construction of complete or nearly complete AMDV sequences, the raw next generation sequencing (NGS) reads were quality-filtered, de novo assembled, and annotated using Trimmomatic, Megahit, and SANSparallel programs, respectively, implemented in Lazypipe pipeline ( Bolger, Lohse, and Usadel 2014 ; Li et al. 2015 ; Somervuo and Holm 2015 ; Plyusnin et al. 2020 ) using default parameters.…”

Section: Methodsmentioning

confidence: 99%

Diversity and transmission of Aleutian mink disease virus in feral and farmed American mink and native mustelids

et al. 2021

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Aleutian mink disease virus (AMDV), which causes Aleutian disease (AD), is widely spread both in farmed mink and wild mustelids. However, only limited data is available on the role of wild animals in AMDV transmission and spread. Our aim was to shed light on AMDV transmission among wild mustelids and estimate the effect of intense farming practices on the virus circulation by studying AMDV prevalence and genetic diversity among wild mustelids in Poland. We compared AMDV seroprevalence and proportion of PCR positive individuals in American mink, polecats, otters, stone martens, and pine martens, and used phylogenetic analysis of NS1 region to study transmission. In addition, we used metagenomic approach to sequence complete AMDV genomes from tissue samples. In eastern Poland, AMDV seroprevalence in wild mustelids varied from 22% in otters to 62% and 64% in stone martens and feral mink, respectively. All studied antibody positive mink were also PCR positive, whereas only 10, 15, and 18% of antibody positive polecats, pine martens, and stone martens, respectively, were PCR positive, suggesting lower virus persistence among these animal species as compared to feral mink. In phylogenetic analysis, most sequences from feral mink formed region-specific clusters that have most likely emerged through multiple introductions of AMDV to feral mink population over decades. However, virus spread between regions was also observed. Virus sequences derived from farmed and wild animals formed separate sub-clusters in the phylogenetic tree and no signs of recent virus transmission between farmed and wild animals was observed despite frequent inflow of farmed mink escapees to wild populations. These results provide new information about the role of different mustelid species in AMDV transmission and about virus circulation among the wild mustelids. In addition, we pinpoint gaps-of-knowledge, where more studies are needed to achieve a comprehensive picture of AMDV transmission.

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Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types

Cited by 36 publications

References 55 publications

Viral RNA Metagenomics of Hyalomma Ticks Collected from Dromedary Camels in Makkah Province, Saudi Arabia

Viral RNA Metagenomics of Hyalomma Ticks Collected from Dromedary Camels in Makkah Province, Saudi Arabia

Human and Animal RNA Virus Diversity Detected by Metagenomics in Cameroonian Clams

Diversity and transmission of Aleutian mink disease virus in feral and farmed American mink and native mustelids

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